| 1985 | | In A Doghouse (2) |
| 1986 | | In A Doghouse (1) |
| 1986 | | Throwing Muses (1) |
| 1987 | | Chains Changed |
| 1987 | | The Fat Skier |
| 1988 | | House Tornado |
| 1989 | | Dizzy |
| 1989 | | Dizzy (Remix) |
| 1989 | | Hunkpapa |
| 1989 | | Live in Brussels, March 1989 at the Ancienne Belgique |
| 1990 | | Not Too Soon |
| 1991 | | Counting Backwards |
| 1991 | | The Real Ramona |
| 1992 | | Firepile (1) |
| 1992 | | Firepile (2) |
| 1992 | | Red Heaven |
| 1992 | | The Curse |
| 1994 | | Bright Yellow Gun |
| 1995 | | University |
| 1996 | | Limbo |
| 1996 | | Ruthie's Knocking |
| 1996 | | Shark |
| 1997 | | Freeloader |
| 2001 | | Live in Providence |
| 2003 | | Throwing Muses |
| 2006 | | Live At The Middle East, Cambridge, MA (August 11, 2006) |
| 2006 | | Live at the Bowery Ballroom |
| 2011 | | Anthology (1) |
| 2011 | | Anthology (2) |
| 2013 | | Purgatory-Paradise |
| 2020 | | Sun Racket |
| 2025 | | Moonlight Concessions |